[Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

[Saeed Mahdizadeh Bakhshmand]

Hello,

Since surface deformation from WM to inflated surface is a gradual process,
I assume that interim surfaces can also be saved and visualized, as I have
seen in the ppt of "Analyzing the Individual Subject
" tutorial
session (slide #32). I am curious to know which command and options can
generate that type of gradual deformations from pial surface to spherical
surface, so that viewer can visually track region or points of interest?

Best,

Saeed
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Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

[Saeed Mahdizadeh Bakhshmand]

Thanks Bruce, and Is there an easy way to make a movie of this deformation?

On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl 
wrote:

> Hi Saeed
>
> if you specify -w  to mris_inflate or mris_sphere it will save snapshots
> of the process every nth iteration
> cheers
> Bruce
>
>
> On Wed, 5 Aug 2015,
> Saeed Mahdizadeh Bakhshmand wrote:
>
> > Hello,
> >
> > Since surface deformation from WM to inflated surface is a gradual
> process,
> > I assume that interim surfaces can also be saved and visualized, as I
> have
> > seen in the ppt of "Analyzing the Individual Subject" tutorial session
> > (slide #32). I am curious to know which command and options can generate
> > that type of gradual deformations from pial surface to spherical
> surface, so
> > that viewer can visually track region or points of interest?
> >
> > Best,
> >
> > Saeed
> >
> >
> >
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>
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Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

[Saeed Mahdizadeh Bakhshmand]

I am a bit confused, "mri_convert" is basically used to convert 3D models
(e.g. .inflate file types) to tiff images? Will it be captured from a
specified perspective and 1 tiff for each volume?
And these tiff files will be combined to generate animated gif? What is
"dynamic gifti"?


On Wed, Aug 5, 2015 at 3:08 PM, Bruce Fischl 
wrote:

> you can use convert to take the multiple tiff files that are written and
> output a dynamic gifti
>
> On Wed, 5 Aug 2015, Saeed
> Mahdizadeh Bakhshmand wrote:
>
> > Thanks Bruce, and Is there an easy way to make a movie of this
> deformation?
> >
> > On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl  >
> > wrote:
> >   Hi Saeed
> >
> >   if you specify -w  to mris_inflate or mris_sphere it will
> >   save snapshots
> >   of the process every nth iteration
> >   cheers
> >   Bruce
> >
> >
> >   On Wed, 5 Aug 2015,
> >   Saeed Mahdizadeh Bakhshmand wrote:
> >
> >   > Hello,
> >   >
> >   > Since surface deformation from WM to inflated surface is a
> >   gradual process,
> >   > I assume that interim surfaces can also be saved and
> >   visualized, as I have
> >   > seen in the ppt of "Analyzing the Individual Subject" tutorial
> >   session
> >   > (slide #32). I am curious to know which command and options
> >   can generate
> >   > that type of gradual deformations from pial surface to
> >   spherical surface, so
> >   > that viewer can visually track region or points of interest?
> >   >
> >   > Best,
> >   >
> >   > Saeed
> >   >
> >   >
> >   >
> > ___
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> >
> >
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> > dispose of the e-mail.
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> >
> >
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[Freesurfer] Label or Overlay of Surface files

[Saeed Mahdizadeh Bakhshmand]

Hello,

Is scalar overlay information embedded into surface file itself? When I
open them in freeview they are loaded with color overlays (sulcus/gyrus),
but when I load same models into 3D slicer or take a snapshot in tksurfer,
they are plain gray.

Thanks,
Saeed
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Re: [Freesurfer] Label or Overlay of Surface files

[Saeed Mahdizadeh Bakhshmand]

And are they treated as label files (e.g. lh.aparc.annot ) in the label
directory? And how they can be added to the tksurfer snapshot procedure?

On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl 
wrote:

> no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc,
> etc...)
>
> On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>
> Hello,
>> Is scalar overlay information embedded into surface file itself? When I
>> open
>> them in freeview they are loaded with color overlays (sulcus/gyrus), but
>> when I load same models into 3D slicer or take a snapshot in tksurfer,
>> they
>> are plain gray.
>>
>> Thanks,
>> Saeed
>>
>>
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Re: [Freesurfer] Label or Overlay of Surface files

[Saeed Mahdizadeh Bakhshmand]

I used it as this:
tksurfer subject hemisphere surface -snap   -overlay 
And it adds a* gray scale* version of sulcus map to the plain gray, How can
I activate colors?

Thanks,
Saeed

On Thu, Aug 6, 2015 at 4:20 PM, Bruce Fischl 
wrote:

> load them as "curvature" files
>
> cheers
> Bruce
>
>
> On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>
> And are they treated as label files (e.g. lh.aparc.annot ) in the label
>> directory? And how they can be added to the tksurfer snapshot procedure?
>>
>> On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl 
>> wrote:
>>   no, the scalar overlays are stored separately (e.g. lh.curv,
>>   lh.sulc, etc...)
>>   On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>>
>> Hello,
>> Is scalar overlay information embedded into surface
>> file itself? When I open
>> them in freeview they are loaded with color overlays
>> (sulcus/gyrus), but
>> when I load same models into 3D slicer or take a
>> snapshot in tksurfer, they
>> are plain gray.
>>
>> Thanks,
>> Saeed
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
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Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

[Saeed Mahdizadeh Bakhshmand]

Hello,

What are your suggested values for *w* and *n* in *mris_sphere*? I set *w*
to 5 and all of the iterations are spheres!

Thanks,
Saeed

On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl 
wrote:

> Hi Saeed
>
> if you specify -w  to mris_inflate or mris_sphere it will save snapshots
> of the process every nth iteration
> cheers
> Bruce
>
>
> On Wed, 5 Aug 2015,
> Saeed Mahdizadeh Bakhshmand wrote:
>
> > Hello,
> >
> > Since surface deformation from WM to inflated surface is a gradual
> process,
> > I assume that interim surfaces can also be saved and visualized, as I
> have
> > seen in the ppt of "Analyzing the Individual Subject" tutorial session
> > (slide #32). I am curious to know which command and options can generate
> > that type of gradual deformations from pial surface to spherical
> surface, so
> > that viewer can visually track region or points of interest?
> >
> > Best,
> >
> > Saeed
> >
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
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Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

[Saeed Mahdizadeh Bakhshmand]

Ok, but how about the mophing process? Isn't inflated brain transformed to
the sphere directly? Is there a middle step that is hidden (e.g. inflatted
to the brain flat maps and spreading these maps over the sphere)? I want to
generate a contineous transformation video from WM to inflated and inflated
to a sphere.
On Aug 6, 2015 7:45 PM, "Bruce Fischl"  wrote:

> yes, because it is unfolding on the sphere to recover metric properties.
> -w 1 gives you every iteration. You will need to show curvature or you
> won't see anything
>
> On Thu, 6 Aug 2015, Saeed Mahdizadeh
> Bakhshmand wrote:
>
> > Hello,
> > What are your suggested values for w and n in mris_sphere? I set w to 5
> and
> > all of the iterations are spheres!
> >
> > Thanks,
> > Saeed
> >
> > On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl  >
> > wrote:
> >   Hi Saeed
> >
> >   if you specify -w  to mris_inflate or mris_sphere it will
> >   save snapshots
> >   of the process every nth iteration
> >   cheers
> >   Bruce
> >
> >
> >   On Wed, 5 Aug 2015,
> >   Saeed Mahdizadeh Bakhshmand wrote:
> >
> >   > Hello,
> >   >
> >   > Since surface deformation from WM to inflated surface is a
> >   gradual process,
> >   > I assume that interim surfaces can also be saved and
> >   visualized, as I have
> >   > seen in the ppt of "Analyzing the Individual Subject" tutorial
> >   session
> >   > (slide #32). I am curious to know which command and options
> >   can generate
> >   > that type of gradual deformations from pial surface to
> >   spherical surface, so
> >   > that viewer can visually track region or points of interest?
> >   >
> >   > Best,
> >   >
> >   > Saeed
> >   >
> >   >
> >   >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
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> >
> >
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> > e-mail
> > contains patient information, please contact the Partners Compliance
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> > but does not contain patient information, please contact the sender
> > and properly
> > dispose of the e-mail.
> >
> >
> >
> >
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Re: [Freesurfer] Label or Overlay of Surface files

[Saeed Mahdizadeh Bakhshmand]

Hi Lee,

Perfect, Thanks.

Saeed

On Thu, Aug 6, 2015 at 5:15 PM, Lee Tirrell 
wrote:

> Hi Saeed,
>
> You can run either of the following commands to overlay the ?h.sulc or
> ?h.curv file:
>
> tksurfer subject hemisphere surface -snap   -sulc
> tksurfer subject hemisphere surface -snap   -curv
>
> Best,
> Lee
>
>
> On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>
> I used it as this:tksurfer subject hemisphere surface -snap  
>> -overlay 
>> And it adds a gray scale version of sulcus map to the plain gray, How can
>> I activate colors?
>>
>> Thanks,
>> Saeed
>>
>> On Thu, Aug 6, 2015 at 4:20 PM, Bruce Fischl 
>> wrote:
>>   load them as "curvature" files
>>
>>   cheers
>>   Bruce
>>
>>   On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>>
>> And are they treated as label files (e.g. lh.aparc.annot ) in
>> the label
>> directory? And how they can be added to the tksurfer snapshot
>> procedure?
>>
>> On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>>     wrote:
>>   no, the scalar overlays are stored separately (e.g.
>> lh.curv,
>>   lh.sulc, etc...)
>>   On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>>
>> Hello,
>> Is scalar overlay information embedded into
>> surface
>> file itself? When I open
>> them in freeview they are loaded with color
>> overlays
>> (sulcus/gyrus), but
>> when I load same models into 3D slicer or take a
>> snapshot in tksurfer, they
>> are plain gray.
>>
>> Thanks,
>> Saeed
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the
>> person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in
>> error and the
>> e-mail
>> contains patient information, please contact the Partners
>> Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was
>> sent to you
>> in error
>> but does not contain patient information, please contact the
>> sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
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>>
>>
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>> is
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>> e-mail
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>>
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Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

[Saeed Mahdizadeh Bakhshmand]

Hello Bruce,

Is there any way to access the table of flag information for mris_sphere? This
page <https://surfer.nmr.mgh.harvard.edu/fswiki/mris_sphere> seems to e
incomplete in that aspect.

Many Thanks,
Saeed

On Fri, Aug 7, 2015 at 10:36 AM, Bruce Fischl 
wrote:

> Hi Saeed
>
> we normally project onto the sphere, but if you want to generate a movie
> to show the idea you can give mris_sphere the flag -i, which will cause it
> to inflate to the sphere before unfolding.
>
> cheers
> Bruce
>
>
> On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>
>
>> Ok, but how about the mophing process? Isn't inflated brain transformed to
>> the sphere directly? Is there a middle step that is hidden (e.g. inflatted
>> to the brain flat maps and spreading these maps over the sphere)? I want
>> to
>> generate a contineous transformation video from WM to inflated and
>> inflated
>> to a sphere.
>>
>> On Aug 6, 2015 7:45 PM, "Bruce Fischl" 
>> wrote:
>>   yes, because it is unfolding on the sphere to recover metric
>>   properties.
>>   -w 1 gives you every iteration. You will need to show curvature
>>   or you
>>   won't see anything
>>
>>   On Thu, 6 Aug 2015, Saeed Mahdizadeh
>>   Bakhshmand wrote:
>>
>>   > Hello,
>>   > What are your suggested values for w and n in mris_sphere? I
>>   set w to 5 and
>>   > all of the iterations are spheres!
>>   >
>>   > Thanks,
>>   > Saeed
>>   >
>>   > On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl
>>   
>>   > wrote:
>>   >   Hi Saeed
>>   >
>>   >   if you specify -w  to mris_inflate or mris_sphere it
>>   will
>>   >   save snapshots
>>   >   of the process every nth iteration
>>   >   cheers
>>   >   Bruce
>>   >
>>   >
>>   >   On Wed, 5 Aug 2015,
>>   >   Saeed Mahdizadeh Bakhshmand wrote:
>>   >
>>   >   > Hello,
>>   >   >
>>   >   > Since surface deformation from WM to inflated surface
>>   is a
>>   >   gradual process,
>>   >   > I assume that interim surfaces can also be saved and
>>   >   visualized, as I have
>>   >   > seen in the ppt of "Analyzing the Individual Subject"
>>   tutorial
>>   >   session
>>   >   > (slide #32). I am curious to know which command and
>>   options
>>   >   can generate
>>   >   > that type of gradual deformations from pial surface to
>>   >   spherical surface, so
>>   >   > that viewer can visually track region or points of
>>   interest?
>>   >   >
>>   >   > Best,
>>   >   >
>>   >   > Saeed
>>   >   >
>>   >   >
>>   >   >
>>   > ___
>>   > Freesurfer mailing list
>>   > Freesurfer@nmr.mgh.harvard.edu
>>   > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>   >
>>   >
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Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

[Saeed Mahdizadeh Bakhshmand]

FS has a lot of hidden capabilities that beginner users (like me) can find
out by reading a proper documentation and save your time for more technical
questions. Documentation doesn't correlate with how great FS and it's
support community is.

On Fri, Aug 7, 2015 at 11:11 AM, Bruce Fischl 
wrote:

> I guess only by looking at the code. We have tried to flesh out most of
> the documentation but have limited resources and person-power (and
> funding!) to do so.
>
> sorry
> Bruce
>
>
>
> On Fri, 7 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>
> Hello Bruce,
>> Is there any way to access the table of flag information for mris_sphere?
>> This page seems to e incomplete in that aspect.
>>
>> Many Thanks,
>> Saeed
>>
>> On Fri, Aug 7, 2015 at 10:36 AM, Bruce Fischl > >
>> wrote:
>>   Hi Saeed
>>
>>   we normally project onto the sphere, but if you want to generate
>>   a movie to show the idea you can give mris_sphere the flag -i,
>>   which will cause it to inflate to the sphere before unfolding.
>>
>>   cheers
>>   Bruce
>>
>>   On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>>
>>
>> Ok, but how about the mophing process? Isn't
>> inflated brain transformed to
>> the sphere directly? Is there a middle step that is
>> hidden (e.g. inflatted
>> to the brain flat maps and spreading these maps over
>> the sphere)? I want to
>> generate a contineous transformation video from WM
>> to inflated and inflated
>> to a sphere.
>>
>> On Aug 6, 2015 7:45 PM, "Bruce Fischl"
>>  wrote:
>>   yes, because it is unfolding on the sphere to
>>     recover metric
>>   properties.
>>   -w 1 gives you every iteration. You will need
>> to show curvature
>>   or you
>>   won't see anything
>>
>>   On Thu, 6 Aug 2015, Saeed Mahdizadeh
>>   Bakhshmand wrote:
>>
>>   > Hello,
>>   > What are your suggested values for w and n
>> in mris_sphere? I
>>   set w to 5 and
>>   > all of the iterations are spheres!
>>   >
>>   > Thanks,
>>   > Saeed
>>   >
>>   > On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl
>>   
>>   > wrote:
>>   >   Hi Saeed
>>       >
>>   >   if you specify -w  to mris_inflate
>> or mris_sphere it
>>   will
>>   >   save snapshots
>>   >   of the process every nth iteration
>>   >   cheers
>>   >   Bruce
>>   >
>>   >
>>   >   On Wed, 5 Aug 2015,
>>   >   Saeed Mahdizadeh Bakhshmand wrote:
>>   >
>>   >   > Hello,
>>   >   >
>>   >   > Since surface deformation from WM to
>> inflated surface
>>   is a
>>   >   gradual process,
>>   >   > I assume that interim surfaces can
>> also be saved and
>>   >   visualized, as I have
>>   >   > seen in the ppt of "Analyzing the
>> Individual Subject"
>>   tutorial
>>   >   session
>>   >   > (slide #32). I am curious to know
>> which command and
>>   options
>>   >   can generate
>>   >   > that type of gradual deformations
>> from pial surface to
>>   >   spherical surface, so
>>   >   > that viewer can visually track
>> region or points of
>>   interest?
>>   >   >
>>   >   > Best,
>>   >   >
>>   > 

Re: [Freesurfer] Label or Overlay of Surface files

[Saeed Mahdizadeh Bakhshmand]

Hello,

I am trying to load surface overlays in 3D Slicer on top of surface meshes
(e.g. lh.Inflated),
but surface overlays somehow don't load properly into 3D slicer, I am
trying right surface files (lh.sulc , lh.curve e.g.)?

On Fri, Aug 7, 2015 at 10:14 AM, Saeed Mahdizadeh Bakhshmand <
saeedbakhshm...@gmail.com> wrote:

> Hi Lee,
>
> Perfect, Thanks.
>
> Saeed
>
> On Thu, Aug 6, 2015 at 5:15 PM, Lee Tirrell 
> wrote:
>
>> Hi Saeed,
>>
>> You can run either of the following commands to overlay the ?h.sulc or
>> ?h.curv file:
>>
>> tksurfer subject hemisphere surface -snap   -sulc
>> tksurfer subject hemisphere surface -snap   -curv
>>
>> Best,
>> Lee
>>
>>
>> On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>>
>> I used it as this:tksurfer subject hemisphere surface -snap  
>>> -overlay 
>>> And it adds a gray scale version of sulcus map to the plain gray, How
>>> can I activate colors?
>>>
>>> Thanks,
>>> Saeed
>>>
>>> On Thu, Aug 6, 2015 at 4:20 PM, Bruce Fischl 
>>> wrote:
>>>   load them as "curvature" files
>>>
>>>   cheers
>>>   Bruce
>>>
>>>   On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>>>
>>> And are they treated as label files (e.g. lh.aparc.annot )
>>> in the label
>>> directory? And how they can be added to the tksurfer
>>> snapshot procedure?
>>>
>>> On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   no, the scalar overlays are stored separately (e.g.
>>> lh.curv,
>>>   lh.sulc, etc...)
>>>   On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>>>
>>> Hello,
>>> Is scalar overlay information embedded into
>>> surface
>>> file itself? When I open
>>> them in freeview they are loaded with color
>>> overlays
>>> (sulcus/gyrus), but
>>> when I load same models into 3D slicer or take a
>>> snapshot in tksurfer, they
>>> are plain gray.
>>>
>>> Thanks,
>>> Saeed
>>>
>>>
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Re: [Freesurfer] Label or Overlay of Surface files

[Saeed Mahdizadeh Bakhshmand]

SOLVED.

On Fri, Aug 14, 2015 at 4:08 PM, Saeed Mahdizadeh Bakhshmand <
saeedbakhshm...@gmail.com> wrote:

> Hello,
>
> I am trying to load surface overlays in 3D Slicer on top of surface meshes
> (e.g. lh.Inflated),
> but surface overlays somehow don't load properly into 3D slicer, I am
> trying right surface files (lh.sulc , lh.curve e.g.)?
>
> On Fri, Aug 7, 2015 at 10:14 AM, Saeed Mahdizadeh Bakhshmand <
> saeedbakhshm...@gmail.com> wrote:
>
>> Hi Lee,
>>
>> Perfect, Thanks.
>>
>> Saeed
>>
>> On Thu, Aug 6, 2015 at 5:15 PM, Lee Tirrell > > wrote:
>>
>>> Hi Saeed,
>>>
>>> You can run either of the following commands to overlay the ?h.sulc or
>>> ?h.curv file:
>>>
>>> tksurfer subject hemisphere surface -snap   -sulc
>>> tksurfer subject hemisphere surface -snap   -curv
>>>
>>> Best,
>>> Lee
>>>
>>>
>>> On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>>>
>>> I used it as this:tksurfer subject hemisphere surface -snap  
>>>> -overlay 
>>>> And it adds a gray scale version of sulcus map to the plain gray, How
>>>> can I activate colors?
>>>>
>>>> Thanks,
>>>> Saeed
>>>>
>>>> On Thu, Aug 6, 2015 at 4:20 PM, Bruce Fischl <
>>>> fis...@nmr.mgh.harvard.edu> wrote:
>>>>   load them as "curvature" files
>>>>
>>>>   cheers
>>>>   Bruce
>>>>
>>>>   On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>>>>
>>>> And are they treated as label files (e.g. lh.aparc.annot )
>>>> in the label
>>>> directory? And how they can be added to the tksurfer
>>>> snapshot procedure?
>>>>
>>>> On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl <
>>>> fis...@nmr.mgh.harvard.edu>
>>>> wrote:
>>>>   no, the scalar overlays are stored separately (e.g.
>>>> lh.curv,
>>>>   lh.sulc, etc...)
>>>>   On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
>>>>
>>>> Hello,
>>>> Is scalar overlay information embedded into
>>>> surface
>>>> file itself? When I open
>>>> them in freeview they are loaded with color
>>>> overlays
>>>> (sulcus/gyrus), but
>>>> when I load same models into 3D slicer or take a
>>>> snapshot in tksurfer, they
>>>> are plain gray.
>>>>
>>>> Thanks,
>>>> Saeed
>>>>
>>>>
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> The information in this e-mail is intended only for the
>>>> person to whom
>>>> it is
>>>> addressed. If you believe this e-mail was sent to you in
>>>> error and the
>>>> e-mail
>>>> contains patient information, please contact the Partners
>>>> Compliance
>>>> HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was
>>>> sent to you
>>>> in error
>>>> but does not contain patient information, please contact
>>>> the sender
>>>> and properly
>>>> dispose of the e-mail.
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[Freesurfer] Brain on a Single Sphere

[Saeed Mahdizadeh Bakhshmand]

Hello Experts,

Is there any command that can map both hemispheres of the brain into one
single sphere? It will be equal to combining two inflated hemispheres into
one spherical brain surface that has its own scalar overlays.

Best,
Saeed
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[Freesurfer] Volumetric measurments and difference between results from "recon_all" and "mri_segstats"

[Saeed Mahdizadeh Bakhshmand]

Hello Folks,

 I used the recon-all -i -all -segmentation for the structural
image. FreeSurfer makes several folder and one of them is "stats". In this
folder, there is aseg.stats that includes volume of different brain
regions. Also, I found "mri_segstats" command line that gives us the volume
of the same brain regions. But, there is significant difference between
reported numbers  from these two methods . I would say the difference is
approximately 200 mm3 for each brain region. Do you know what is correct
way to measure volume of segmented brain regions using FreeSurfer?

Cheers,
Saeed
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[Freesurfer] (no subject)

[Saeed Mahdizadeh Bakhshmand]

Hello,

As we know, Freesurfer generates separate surface models and associated
labels for each brain hemisphere, is there any way to merge two hemisphere
and come up with a single cortex surface?

My best,
Saeed
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[Freesurfer] Merging Brain Hemispheres

[Saeed Mahdizadeh Bakhshmand]

Hello,

As we know, Freesurfer generates separate surface models and associated
labels for each brain hemisphere, is there any way to merge two hemisphere
and come up with a single cortex surface?

My best,
Saeed

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